ANSWER05 IRIX (gcg2) login: petang Password: gcg2 1% go gcg2 2% mkdir LECTURE5 gcg2 3% ls CASPASE CeLR LECTURE5 RACE TVCDC WEIMIN CP DAT PRACTICE SEQUENCING TVLDLR gcg2 4% cd LECTURE5 gcg2 5% fetch genbank:k02938 Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. k02938.gb_ov gcg2 6% fetch genbank:x15785 Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. x15785.gb_ov gcg2 7% bestfit BestFit makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman. BESTFIT of what sequence 1 ? k02938.gb_ov Begin (* 1 *) ? End (* 1518 *) ? Reverse (* No *) ? to what sequence 2 (* k02938.gb_ov *) ? x15785.gb_ov Begin (* 1 *) ? End (* 515 *) ? Reverse (* No *) ? What is the gap creation penalty (* 50 *) ? What is the gap extension penalty (* 3 *) ? What should I call the paired output display file (* k02938.pair *) ? best.pai r Aligning .........................-. Aligning .........................-. Gaps: 0 Quality: 654 Quality Ratio: 8.959 % Similarity: 94.521 Length: 73 gcg2 8% cat best.pair BESTFIT of: k02938.gb_ov check: 6524 from: 1 to: 1518 LOCUS XELTFIIIA 1518 bp mRNA VRT 28-APR-1993 DEFINITION X.laevis 5S RNA gene transcription factor (TFIIIA) mRNA, complete cds. ACCESSION K02938 VERSION K02938.1 GI:214818 KEYWORDS developmental regulation; transcription factor. . . . to: x15785.gb_ov check: 238 from: 1 to: 515 LOCUS XLTF3A5 515 bp DNA VRT 03-DEC-1998 DEFINITION Xenopus laevis TFIIIA gene 5' region and partial coding region. ACCESSION X15785 VERSION X15785.1 GI:65120 KEYWORDS developmental regulation; TFIIIA gene; transcription factor; transcription factor IIIA; zinc finger protein. . . . Symbol comparison table: /usr/people/gcg/gcgcore/data/rundata/swgapdna.cmp CompCheck: 2335 Gap Weight: 50 Average Match: 10.000 Length Weight: 3 Average Mismatch: -9.000 Quality: 654 Length: 73 Ratio: 8.959 Gaps: 0 Percent Similarity: 94.521 Percent Identity: 94.521 Match display thresholds for the alignment(s): | = IDENTITY : = 5 . = 1 k02938.gb_ov x x15785.gb_ov March 24, 2000 01:14 .. . . . . . 8 GGAAGCCGAGGGCTGTTCAGTTGCTGAAGGAGAGATGGGAGAGAAGGCGC 57 ||||||||||||| | | |||| ||||||||||||||||||||||||||| 443 GGAAGCCGAGGGCAGCTTAGTTACTGAAGGAGAGATGGGAGAGAAGGCGC 492 . . 58 TGCCGGTGGTGTATAAGCGGTAC 80 ||||||||||||||||||||||| 493 TGCCGGTGGTGTATAAGCGGTAC 515 gcg2 9% gap Gap uses the algorithm of Needleman and Wunsch to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP of what sequence 1 ? k02938.gb_ov Begin (* 1 *) ? End (* 1518 *) ? Reverse (* No *) ? to what sequence 2 (* k02938.gb_ov *) ? x15785.gb_ov Begin (* 1 *) ? End (* 515 *) ? Reverse (* No *) ? What is the gap creation penalty (* 50 *) ? What is the gap extension penalty (* 3 *) ? What should I call the paired output display file (* k02938.pair *) ? gap.pair Aligning .........................-. Aligning .........................-... Gaps: 2 Quality: 1789 Quality Ratio: 3.474 % Similarity: 37.160 Length: 1519 gcg2 10% cat gap.pair GAP of: k02938.gb_ov check: 6524 from: 1 to: 1518 LOCUS XELTFIIIA 1518 bp mRNA VRT 28-APR-1993 DEFINITION X.laevis 5S RNA gene transcription factor (TFIIIA) mRNA, complete cds. ACCESSION K02938 VERSION K02938.1 GI:214818 KEYWORDS developmental regulation; transcription factor. . . . to: x15785.gb_ov check: 238 from: 1 to: 515 LOCUS XLTF3A5 515 bp DNA VRT 03-DEC-1998 DEFINITION Xenopus laevis TFIIIA gene 5' region and partial coding region. ACCESSION X15785 VERSION X15785.1 GI:65120 KEYWORDS developmental regulation; TFIIIA gene; transcription factor; transcription factor IIIA; zinc finger protein. . . . Symbol comparison table: /usr/people/gcg/gcgcore/data/rundata/nwsgapdna.cmp CompCheck: 8760 Gap Weight: 50 Average Match: 10.000 Length Weight: 3 Average Mismatch: 0.000 Quality: 1789 Length: 1519 Ratio: 3.474 Gaps: 2 Percent Similarity: 37.160 Percent Identity: 37.160 Match display thresholds for the alignment(s): | = IDENTITY : = 5 . = 1 k02938.gb_ov x x15785.gb_ov March 24, 2000 01:16 .. . . . . . . . . 301 AGGCAAACATGAAGAAGCACTTTAACAGATTCCATAACATCAAGATCTGC 350 | || | | | | | || | | | 1 ..............AGATCTATTGAGAAAGGGCCTTACTGTGTGCTGTAA 36 . . . . . 351 GTCTATG.TGTGCCATTTTGAGAACTGTGGCAAAGCATTCAAGAAACACA 399 | ||| ||| | | | | | | |||| | | 37 TTAGATGCTGTTAGTTATCGCACTCCTGTGTGGACCATTGCATCCATCAC 86 . . . . . 400 ATCAATTAAAGGTTCATCAGTTCAGTCACACACAGCAGCTGCCATACGAA 449 || | | || | || || ||| |||| ||||| || 87 ATTCACAACAGTTACAGTTTCTCCAACACCAGCAGCTGCTGCACACCGTT 136 . . . . . 450 TGTCCTCATGAAGGCTGTGACAAGCGGTTTTCTTTGCCTTCCCGTTTAAA 499 | | | | | | || | | | || | || | ||| 137 TCCTCGGCTTCATGTATTATCACGTGCTCCACTAGGACTCAACCACTAAG 186 . . . . . 500 ACGTCATGAAAAAGTCCATGCAGGCTATCCCTGCAAAAAGGATGATTCTT 549 | | | | | | | ||| | | || 187 AACGAGGGGAGTGTCCAGAAACACCCAACTTGTGAAATAACACATCGCTG 236 . . . . . 550 GCTCATTTGTGGGAAAGACTTGGACATTATACTTGAAACACGTGGCAGAA 599 | | | || | || | || | || || 237 ACATAAAACACAGGAATTTAACATCCTTTTTTTTAAGTTTGCGAGCGCAA 286 . . . . . 600 TGCCATCAGGACCTAGCAGTATGTGATGTGTGTAATCGAAAATTCAGGCA 649 | | ||| ||| | | | || | || | ||| 287 TTACTGAAGGCTAAAGCTGCAAGGGACACAGGAAAGGGCTGATTGCCAAT 336 . . . . . 650 CAAAGATTACTTGAGGGATCATCAGAAAACTCACGAAAAAGAGCGAACTG 699 | || | | | || | | | | | | || | 337 CCTTTCAGACATCGCAAAACTTC......CCGATGCATGTGCGATAATGG 380 . . . . . 700 TGTATCTCTGCCCTCGAGATGGCTGTGACCGCTCCTATACCACTGCATTC 749 | | || | || | | | | | || || ||| 381 TTTGTCCTAGAGCTATATAAACAGGCACACATGGCGGCTACAGTGGCTTC 430 . . . . . 750 AATCTTAGAAGCCATATACAATCATTTCATGAGGAACAGAGACCTTTTGT 799 | || | | | | | | || || 431 TACAAGTTCAGAGGAAGCCGAGGGCAGCTTAGTTACTGAAGGAGAGATGG 480 . . . . . 800 TTGTGAGCATGCTGGCTGCGGGAAATGCTTTGCAATGAAAAAAAGCCTAG 849 | || |||| | | || || | | 481 GAGAGAAGGCGCTGCCGGTGGTGTATAAGCGGTAC............... 515 . . .